Exploring evolution genome-wide in stickleback using RAD-seq

Our understanding of the biological world was revolutionized in 1996 by the sequencing of the first complete genome of an organism. Because of the high cost of DNA sequencing, research in this first genomics phase focused on traditional laboratory model organisms. Technological advances in sequencing over the last five years have led to an open source genomics revolution, in which sequencing has become much more economical and has moved from large genome centers to individual laboratories. Furthermore, these new sequencing technologies are easily modified to produce tools tailored to biological problems. I will describe discoveries about the genomic and transcriptomic basis of rapid evolution in threespine stickleback populations using one such technique, Restriction site Associated DNA sequencing (RAD-seq). This technique allows the simultaneous identification and typing of thousands of single nucleotide polymorphisms (SNPs) as well as the identification of allele specific gene expression. I will also discuss the use of our software pipeline Stacks for the analysis of RAD-seq data in organisms without a reference genome to underscore how non-model organisms can be ‘genomically enabled’ within a single lab to open exciting new research avenues.